003_diff_exp
Me
06/12/2021
Within Guy11
Differential peptide abundance
Perform differential abundance estimation using bootstrap and rank product methods
library(pepdiff)
d <- import_data(here::here("cleaned", "cleaned_data.csv"),
gene_id = "molecule_list_name",
treatment = "genotype",
peptide = "peptide_modified_sequence",
seconds = "timepoint")## Rows: 20520 Columns: 7## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): molecule_list_name, peptide_modified_sequence, genotype
## dbl (4): timepoint, bio_rep, tech_rep, total_area##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.comparisons <- data.frame(
control = rep("Guy11", 5),
c_seconds = rep(0, 5),
treatment = rep("Guy11", 5),
t_seconds = c(1,1.5,2,4,6)
)
many <- compare_many(d, comparisons, metrics = c("bootstrap_t", "rank_product"), iters=10000)## Rank Product analysis for unpaired case
##
##
## done Rank Product analysis for unpaired case
##
##
## done Rank Product analysis for unpaired case
##
##
## done Rank Product analysis for unpaired case
##
##
## done Rank Product analysis for unpaired case
##
##
## donemany## $`Guy11_1-Guy11_0`
## # A tibble: 285 × 31
## gene_id peptide Guy11_1_1 Guy11_1_2 Guy11_1_3 Guy11_1.5_1 Guy11_1.5_2
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|1456017… KLS[+80]AS… 0.000280 0.000330 0.000298 0.000745 0.000225
## 2 gi|1456017… KLSASGS[+8… 0.00269 0.00348 0.00257 0.00285 0.00312
## 3 gi|1456020… QTRT[+80]P… 0.00161 0.00121 0.00148 0.00243 0.000665
## 4 gi|1456020… TPS[+80]PA… 0.00347 0.00198 0.00406 0.00356 0.00334
## 5 gi|1456020… NAFLFGEVTT… 0.000497 0.000686 0.00111 0.000730 0.000967
## 6 gi|1456023… AAEEDVTTT[… 0.0000318 0.0000318 0.0000318 0.0000318 0.0000318
## 7 gi|1456023… VQGNAYGGTG… 0.0000971 0.0000971 0.000290 0.000382 0.000526
## 8 gi|1456026… AVGS[+80]R… 0.00362 0.00695 0.00838 0.00618 0.00766
## 9 gi|1456026… AVGSRS[+80… 0.00370 0.00701 0.00834 0.00625 0.00761
## 10 gi|1456026… DRS[+80]SG… 0.00195 0.000336 0.00170 0.00354 0.00107
## # … with 275 more rows, and 24 more variables: Guy11_1.5_3 <dbl>,
## # Guy11_0_1 <dbl>, Guy11_0_2 <dbl>, Guy11_0_3 <dbl>, fold_change <dbl>,
## # treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_Guy11_1_1 <dbl>, unreplaced_Guy11_1_2 <dbl>,
## # unreplaced_Guy11_1_3 <dbl>, unreplaced_Guy11_1.5_1 <dbl>,
## # unreplaced_Guy11_1.5_2 <dbl>, unreplaced_Guy11_1.5_3 <dbl>,
## # unreplaced_Guy11_0_1 <dbl>, unreplaced_Guy11_0_2 <dbl>, …
##
## $`Guy11_1.5-Guy11_0`
## # A tibble: 285 × 25
## gene_id peptide Guy11_1.5_1 Guy11_1.5_2 Guy11_1.5_3 Guy11_0_1 Guy11_0_2
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|145601… KLS[+80]A… 0.000745 0.000225 0.000117 0.00108 0.000404
## 2 gi|145601… KLSASGS[+… 0.00285 0.00312 0.00168 0.00215 0.00260
## 3 gi|145602… QTRT[+80]… 0.00243 0.000665 0.000749 0.00287 0.00222
## 4 gi|145602… TPS[+80]P… 0.00356 0.00334 0.00297 0.00128 0.00158
## 5 gi|145602… NAFLFGEVT… 0.000730 0.000967 0.000520 0.000608 0.000626
## 6 gi|145602… AAEEDVTTT… 0.0000318 0.0000318 0.0000318 0.0000318 0.0000318
## 7 gi|145602… VQGNAYGGT… 0.000382 0.000526 0.000272 0.0000971 0.0000971
## 8 gi|145602… AVGS[+80]… 0.00618 0.00766 0.00518 0.00193 0.00167
## 9 gi|145602… AVGSRS[+8… 0.00625 0.00761 0.00518 0.00197 0.00167
## 10 gi|145602… DRS[+80]S… 0.00354 0.00107 0.00190 0.000275 0.000275
## # … with 275 more rows, and 18 more variables: Guy11_0_3 <dbl>,
## # fold_change <dbl>, treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_Guy11_1.5_1 <dbl>, unreplaced_Guy11_1.5_2 <dbl>,
## # unreplaced_Guy11_1.5_3 <dbl>, unreplaced_Guy11_0_1 <dbl>,
## # unreplaced_Guy11_0_2 <dbl>, unreplaced_Guy11_0_3 <dbl>,
## # treatment_replicates <int>, control_replicates <int>,
## # bootstrap_t_p_val <dbl>, bootstrap_t_fdr <dbl>, rank_prod_p2_p_val <dbl>, …
##
## $`Guy11_2-Guy11_0`
## # A tibble: 285 × 25
## gene_id peptide Guy11_2_1 Guy11_2_2 Guy11_2_3 Guy11_0_1 Guy11_0_2 Guy11_0_3
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|1456… KLS[+80… 0.000143 0.000174 0.000578 0.00108 0.000404 0.0000917
## 2 gi|1456… KLSASGS… 0.00155 0.00261 0.00122 0.00215 0.00260 0.00164
## 3 gi|1456… QTRT[+8… 0.00233 0.00110 0.00135 0.00287 0.00222 0.000471
## 4 gi|1456… TPS[+80… 0.00339 0.00377 0.00356 0.00128 0.00158 0.000209
## 5 gi|1456… NAFLFGE… 0.000840 0.00107 0.000352 0.000608 0.000626 0.000501
## 6 gi|1456… AAEEDVT… 0.0000318 0.000252 0.0000318 0.0000318 0.0000318 0.0000318
## 7 gi|1456… VQGNAYG… 0.0000971 0.00135 0.00111 0.0000971 0.0000971 0.0000971
## 8 gi|1456… AVGS[+8… 0.000938 0.00144 0.00358 0.00193 0.00167 0.00936
## 9 gi|1456… AVGSRS[… 0.000938 0.00144 0.00358 0.00197 0.00167 0.00934
## 10 gi|1456… DRS[+80… 0.00140 0.00130 0.00445 0.000275 0.000275 0.000275
## # … with 275 more rows, and 17 more variables: fold_change <dbl>,
## # treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_Guy11_2_1 <dbl>, unreplaced_Guy11_2_2 <dbl>,
## # unreplaced_Guy11_2_3 <dbl>, unreplaced_Guy11_0_1 <dbl>,
## # unreplaced_Guy11_0_2 <dbl>, unreplaced_Guy11_0_3 <dbl>,
## # treatment_replicates <int>, control_replicates <int>,
## # bootstrap_t_p_val <dbl>, bootstrap_t_fdr <dbl>, rank_prod_p2_p_val <dbl>, …
##
## $`Guy11_4-Guy11_0`
## # A tibble: 285 × 25
## gene_id peptide Guy11_4_1 Guy11_4_2 Guy11_4_3 Guy11_0_1 Guy11_0_2 Guy11_0_3
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|1456… KLS[+80… 0.00125 0.000264 0.000475 0.00108 0.000404 0.0000917
## 2 gi|1456… KLSASGS… 0.00298 0.00202 0.00228 0.00215 0.00260 0.00164
## 3 gi|1456… QTRT[+8… 0.00184 0.00116 0.000869 0.00287 0.00222 0.000471
## 4 gi|1456… TPS[+80… 0.00514 0.00371 0.00457 0.00128 0.00158 0.000209
## 5 gi|1456… NAFLFGE… 0.00184 0.00153 0.00166 0.000608 0.000626 0.000501
## 6 gi|1456… AAEEDVT… 0.0000318 0.000194 0.000111 0.0000318 0.0000318 0.0000318
## 7 gi|1456… VQGNAYG… 0.00449 0.00400 0.00538 0.0000971 0.0000971 0.0000971
## 8 gi|1456… AVGS[+8… 0.0196 0.0128 0.00810 0.00193 0.00167 0.00936
## 9 gi|1456… AVGSRS[… 0.0197 0.0128 0.00818 0.00197 0.00167 0.00934
## 10 gi|1456… DRS[+80… 0.00845 0.00328 0.00431 0.000275 0.000275 0.000275
## # … with 275 more rows, and 17 more variables: fold_change <dbl>,
## # treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_Guy11_4_1 <dbl>, unreplaced_Guy11_4_2 <dbl>,
## # unreplaced_Guy11_4_3 <dbl>, unreplaced_Guy11_0_1 <dbl>,
## # unreplaced_Guy11_0_2 <dbl>, unreplaced_Guy11_0_3 <dbl>,
## # treatment_replicates <int>, control_replicates <int>,
## # bootstrap_t_p_val <dbl>, bootstrap_t_fdr <dbl>, rank_prod_p2_p_val <dbl>, …
##
## $`Guy11_6-Guy11_0`
## # A tibble: 285 × 25
## gene_id peptide Guy11_6_1 Guy11_6_2 Guy11_6_3 Guy11_0_1 Guy11_0_2 Guy11_0_3
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|1456… KLS[+80… 0.0000917 0.000129 0.000127 0.00108 0.000404 0.0000917
## 2 gi|1456… KLSASGS… 0.000851 0.00129 0.000982 0.00215 0.00260 0.00164
## 3 gi|1456… QTRT[+8… 0.00264 0.000487 0.00362 0.00287 0.00222 0.000471
## 4 gi|1456… TPS[+80… 0.00430 0.00227 0.00558 0.00128 0.00158 0.000209
## 5 gi|1456… NAFLFGE… 0.000588 0.00185 0.000952 0.000608 0.000626 0.000501
## 6 gi|1456… AAEEDVT… 0.000450 0.000128 0.000647 0.0000318 0.0000318 0.0000318
## 7 gi|1456… VQGNAYG… 0.00184 0.00203 0.00158 0.0000971 0.0000971 0.0000971
## 8 gi|1456… AVGS[+8… 0.00123 0.0111 0.000650 0.00193 0.00167 0.00936
## 9 gi|1456… AVGSRS[… 0.00123 0.0111 0.000650 0.00197 0.00167 0.00934
## 10 gi|1456… DRS[+80… 0.00335 0.00211 0.00349 0.000275 0.000275 0.000275
## # … with 275 more rows, and 17 more variables: fold_change <dbl>,
## # treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_Guy11_6_1 <dbl>, unreplaced_Guy11_6_2 <dbl>,
## # unreplaced_Guy11_6_3 <dbl>, unreplaced_Guy11_0_1 <dbl>,
## # unreplaced_Guy11_0_2 <dbl>, unreplaced_Guy11_0_3 <dbl>,
## # treatment_replicates <int>, control_replicates <int>,
## # bootstrap_t_p_val <dbl>, bootstrap_t_fdr <dbl>, rank_prod_p2_p_val <dbl>, …Plot result heatmaps
lgd <- ComplexHeatmap::Legend(direction = "horizontal",
col_fun = circlize::colorRamp2(
seq(-2, 2, length.out = 11),
rev(RColorBrewer::brewer.pal(11, "RdBu"))
),
title = "Log 2 Fold Change")
plot_heatmap(many, metric = "bootstrap_t", log = TRUE)#, col_order = col_order)## Joining, by = "comparison"## Joining, by = "gene_peptide"ComplexHeatmap::draw(lgd, x = grid::unit(8, "in"), y = grid::unit(1, "in"))
plot_heatmap(many, metric = "rank_product", log = TRUE)## Joining, by = "comparison"
## Joining, by = "gene_peptide"ComplexHeatmap::draw(lgd, x = grid::unit(8, "in"), y = grid::unit(1, "in"))
#add colour even when the point isn't significant
plot_heatmap(many, metric = "bootstrap_t", log = TRUE)#, col_order = col_order, only_sig_points = FALSE)## Joining, by = "comparison"## Joining, by = "gene_peptide"ComplexHeatmap::draw(lgd, x = grid::unit(8, "in"), y = grid::unit(1, "in"))
volcano_plot(many, metric = "bootstrap_t")
writexl::write_xlsx(many, here::here("analysis","003_differential_abundance_Guy11_w_geno_estimates.xlsx"))Within dpmk1
comparisons <- data.frame(
control = rep("dpmk1", 5),
c_seconds = rep(0, 5),
treatment = rep("dpmk1", 5),
t_seconds = c(1,1.5,2,4,6)
)
many <- compare_many(d, comparisons, metrics = c("bootstrap_t", "rank_product"), iters=10000)## Rank Product analysis for unpaired case
##
##
## done Rank Product analysis for unpaired case
##
##
## done Rank Product analysis for unpaired case
##
##
## done Rank Product analysis for unpaired case
##
##
## done Rank Product analysis for unpaired case
##
##
## donemany## $`dpmk1_1-dpmk1_0`
## # A tibble: 285 × 31
## gene_id peptide dpmk1_1_1 dpmk1_1_2 dpmk1_1_3 dpmk1_1.5_1 dpmk1_1.5_2
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|1456017… KLS[+80]AS… 0.000308 0.000281 0.000335 0.000456 0.000157
## 2 gi|1456017… KLSASGS[+8… 0.00202 0.00157 0.00455 0.00226 0.00200
## 3 gi|1456020… QTRT[+80]P… 0.000876 0.00201 0.00139 0.00113 0.000698
## 4 gi|1456020… TPS[+80]PA… 0.00240 0.00240 0.00231 0.00334 0.00178
## 5 gi|1456020… NAFLFGEVTT… 0.00102 0.00123 0.00317 0.000900 0.000719
## 6 gi|1456023… AAEEDVTTT[… 0.0000318 0.0000318 0.0000318 0.0000318 0.0000318
## 7 gi|1456023… VQGNAYGGTG… 0.000107 0.000365 0.000286 0.000351 0.000645
## 8 gi|1456026… AVGS[+80]R… 0.00422 0.00564 0.0171 0.0110 0.00557
## 9 gi|1456026… AVGSRS[+80… 0.00424 0.00566 0.0172 0.0110 0.00561
## 10 gi|1456026… DRS[+80]SG… 0.000721 0.00150 0.000447 0.00155 0.00257
## # … with 275 more rows, and 24 more variables: dpmk1_1.5_3 <dbl>,
## # dpmk1_0_1 <dbl>, dpmk1_0_2 <dbl>, dpmk1_0_3 <dbl>, fold_change <dbl>,
## # treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_dpmk1_1_1 <dbl>, unreplaced_dpmk1_1_2 <dbl>,
## # unreplaced_dpmk1_1_3 <dbl>, unreplaced_dpmk1_1.5_1 <dbl>,
## # unreplaced_dpmk1_1.5_2 <dbl>, unreplaced_dpmk1_1.5_3 <dbl>,
## # unreplaced_dpmk1_0_1 <dbl>, unreplaced_dpmk1_0_2 <dbl>, …
##
## $`dpmk1_1.5-dpmk1_0`
## # A tibble: 285 × 25
## gene_id peptide dpmk1_1.5_1 dpmk1_1.5_2 dpmk1_1.5_3 dpmk1_0_1 dpmk1_0_2
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|145601… KLS[+80]A… 0.000456 0.000157 0.0000917 0.00123 0.000316
## 2 gi|145601… KLSASGS[+… 0.00226 0.00200 0.00160 0.000732 0.000321
## 3 gi|145602… QTRT[+80]… 0.00113 0.000698 0.000195 0.00304 0.00271
## 4 gi|145602… TPS[+80]P… 0.00334 0.00178 0.000529 0.000498 0.000462
## 5 gi|145602… NAFLFGEVT… 0.000900 0.000719 0.000654 0.000306 0.000484
## 6 gi|145602… AAEEDVTTT… 0.0000318 0.0000318 0.0000318 0.0000318 0.0000318
## 7 gi|145602… VQGNAYGGT… 0.000351 0.000645 0.000387 0.0000971 0.0000971
## 8 gi|145602… AVGS[+80]… 0.0110 0.00557 0.0102 0.0297 0.0106
## 9 gi|145602… AVGSRS[+8… 0.0110 0.00561 0.0102 0.0296 0.0105
## 10 gi|145602… DRS[+80]S… 0.00155 0.00257 0.000440 0.000275 0.000275
## # … with 275 more rows, and 18 more variables: dpmk1_0_3 <dbl>,
## # fold_change <dbl>, treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_dpmk1_1.5_1 <dbl>, unreplaced_dpmk1_1.5_2 <dbl>,
## # unreplaced_dpmk1_1.5_3 <dbl>, unreplaced_dpmk1_0_1 <dbl>,
## # unreplaced_dpmk1_0_2 <dbl>, unreplaced_dpmk1_0_3 <dbl>,
## # treatment_replicates <int>, control_replicates <int>,
## # bootstrap_t_p_val <dbl>, bootstrap_t_fdr <dbl>, rank_prod_p2_p_val <dbl>, …
##
## $`dpmk1_2-dpmk1_0`
## # A tibble: 285 × 25
## gene_id peptide dpmk1_2_1 dpmk1_2_2 dpmk1_2_3 dpmk1_0_1 dpmk1_0_2 dpmk1_0_3
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|1456… KLS[+80… 0.000251 0.0000917 0.000352 0.00123 0.000316 0.0000917
## 2 gi|1456… KLSASGS… 0.00145 0.00197 0.00464 0.000732 0.000321 0.000321
## 3 gi|1456… QTRT[+8… 0.00123 0.000270 0.00171 0.00304 0.00271 0.000242
## 4 gi|1456… TPS[+80… 0.00246 0.00262 0.00375 0.000498 0.000462 0.00138
## 5 gi|1456… NAFLFGE… 0.000849 0.000837 0.00234 0.000306 0.000484 0.000206
## 6 gi|1456… AAEEDVT… 0.0000318 0.0000318 0.0000318 0.0000318 0.0000318 0.0000318
## 7 gi|1456… VQGNAYG… 0.000275 0.00370 0.00145 0.0000971 0.0000971 0.0000971
## 8 gi|1456… AVGS[+8… 0.00872 0.00601 0.0144 0.0297 0.0106 0.00329
## 9 gi|1456… AVGSRS[… 0.00866 0.00606 0.0144 0.0296 0.0105 0.00329
## 10 gi|1456… DRS[+80… 0.00106 0.00491 0.00193 0.000275 0.000275 0.000275
## # … with 275 more rows, and 17 more variables: fold_change <dbl>,
## # treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_dpmk1_2_1 <dbl>, unreplaced_dpmk1_2_2 <dbl>,
## # unreplaced_dpmk1_2_3 <dbl>, unreplaced_dpmk1_0_1 <dbl>,
## # unreplaced_dpmk1_0_2 <dbl>, unreplaced_dpmk1_0_3 <dbl>,
## # treatment_replicates <int>, control_replicates <int>,
## # bootstrap_t_p_val <dbl>, bootstrap_t_fdr <dbl>, rank_prod_p2_p_val <dbl>, …
##
## $`dpmk1_4-dpmk1_0`
## # A tibble: 285 × 25
## gene_id peptide dpmk1_4_1 dpmk1_4_2 dpmk1_4_3 dpmk1_0_1 dpmk1_0_2 dpmk1_0_3
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|1456… KLS[+80… 0.000447 0.000671 0.000263 0.00123 0.000316 0.0000917
## 2 gi|1456… KLSASGS… 0.00276 0.00395 0.00294 0.000732 0.000321 0.000321
## 3 gi|1456… QTRT[+8… 0.000959 0.000550 0.000818 0.00304 0.00271 0.000242
## 4 gi|1456… TPS[+80… 0.00407 0.00296 0.00310 0.000498 0.000462 0.00138
## 5 gi|1456… NAFLFGE… 0.00306 0.00160 0.00281 0.000306 0.000484 0.000206
## 6 gi|1456… AAEEDVT… 0.000367 0.0000750 0.000265 0.0000318 0.0000318 0.0000318
## 7 gi|1456… VQGNAYG… 0.00607 0.00776 0.00710 0.0000971 0.0000971 0.0000971
## 8 gi|1456… AVGS[+8… 0.0180 0.0160 0.0178 0.0297 0.0106 0.00329
## 9 gi|1456… AVGSRS[… 0.0179 0.0161 0.0178 0.0296 0.0105 0.00329
## 10 gi|1456… DRS[+80… 0.00375 0.00755 0.00298 0.000275 0.000275 0.000275
## # … with 275 more rows, and 17 more variables: fold_change <dbl>,
## # treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_dpmk1_4_1 <dbl>, unreplaced_dpmk1_4_2 <dbl>,
## # unreplaced_dpmk1_4_3 <dbl>, unreplaced_dpmk1_0_1 <dbl>,
## # unreplaced_dpmk1_0_2 <dbl>, unreplaced_dpmk1_0_3 <dbl>,
## # treatment_replicates <int>, control_replicates <int>,
## # bootstrap_t_p_val <dbl>, bootstrap_t_fdr <dbl>, rank_prod_p2_p_val <dbl>, …
##
## $`dpmk1_6-dpmk1_0`
## # A tibble: 285 × 25
## gene_id peptide dpmk1_6_1 dpmk1_6_2 dpmk1_6_3 dpmk1_0_1 dpmk1_0_2 dpmk1_0_3
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 gi|1456… KLS[+80… 0.000101 0.0000992 0.000278 0.00123 0.000316 0.0000917
## 2 gi|1456… KLSASGS… 0.00163 0.000856 0.00132 0.000732 0.000321 0.000321
## 3 gi|1456… QTRT[+8… 0.000110 0.00323 0.000200 0.00304 0.00271 0.000242
## 4 gi|1456… TPS[+80… 0.00130 0.00591 0.00147 0.000498 0.000462 0.00138
## 5 gi|1456… NAFLFGE… 0.00108 0.000803 0.00335 0.000306 0.000484 0.000206
## 6 gi|1456… AAEEDVT… 0.0000318 0.000391 0.0000318 0.0000318 0.0000318 0.0000318
## 7 gi|1456… VQGNAYG… 0.00312 0.00126 0.00280 0.0000971 0.0000971 0.0000971
## 8 gi|1456… AVGS[+8… 0.0160 0.00160 0.0290 0.0297 0.0106 0.00329
## 9 gi|1456… AVGSRS[… 0.0158 0.00162 0.0290 0.0296 0.0105 0.00329
## 10 gi|1456… DRS[+80… 0.00305 0.00360 0.00451 0.000275 0.000275 0.000275
## # … with 275 more rows, and 17 more variables: fold_change <dbl>,
## # treatment_mean_count <dbl>, control_mean_count <dbl>,
## # unreplaced_dpmk1_6_1 <dbl>, unreplaced_dpmk1_6_2 <dbl>,
## # unreplaced_dpmk1_6_3 <dbl>, unreplaced_dpmk1_0_1 <dbl>,
## # unreplaced_dpmk1_0_2 <dbl>, unreplaced_dpmk1_0_3 <dbl>,
## # treatment_replicates <int>, control_replicates <int>,
## # bootstrap_t_p_val <dbl>, bootstrap_t_fdr <dbl>, rank_prod_p2_p_val <dbl>, …Plot result heatmaps
lgd <- ComplexHeatmap::Legend(direction = "horizontal",
col_fun = circlize::colorRamp2(
seq(-2, 2, length.out = 11),
rev(RColorBrewer::brewer.pal(11, "RdBu"))
),
title = "Log 2 Fold Change")
plot_heatmap(many, metric = "bootstrap_t", log = TRUE)#, col_order = col_order)## Joining, by = "comparison"## Joining, by = "gene_peptide"ComplexHeatmap::draw(lgd, x = grid::unit(8, "in"), y = grid::unit(1, "in"))
plot_heatmap(many, metric = "rank_product", log = TRUE)## Joining, by = "comparison"
## Joining, by = "gene_peptide"ComplexHeatmap::draw(lgd, x = grid::unit(8, "in"), y = grid::unit(1, "in"))
#add colour even when the point isn't significant
plot_heatmap(many, metric = "bootstrap_t", log = TRUE)#, col_order = col_order, only_sig_points = FALSE)## Joining, by = "comparison"## Joining, by = "gene_peptide"ComplexHeatmap::draw(lgd, x = grid::unit(8, "in"), y = grid::unit(1, "in"))
volcano_plot(many, metric = "bootstrap_t")
writexl::write_xlsx(many, here::here("analysis","003_differential_abundance_dpmk_w_geno_estimates.xlsx"))